Multiple sequence alignment - TraesCS1D01G006300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS1D01G006300 chr1D 100.000 5309 0 0 1 5309 2889794 2884486 0.000000e+00 9804.0
1 TraesCS1D01G006300 chr1D 87.113 2910 335 25 1348 4235 2717167 2720058 0.000000e+00 3260.0
2 TraesCS1D01G006300 chr1D 77.115 1927 378 44 2228 4120 12534043 12535940 0.000000e+00 1057.0
3 TraesCS1D01G006300 chr1D 88.102 706 65 8 4259 4949 363278144 363277443 0.000000e+00 821.0
4 TraesCS1D01G006300 chr1D 84.725 563 80 6 3699 4258 2477994 2477435 4.640000e-155 558.0
5 TraesCS1D01G006300 chr1D 75.304 575 132 8 1405 1973 12533100 12533670 3.150000e-67 267.0
6 TraesCS1D01G006300 chr1D 83.969 262 31 7 1024 1275 2716899 2717159 1.910000e-59 241.0
7 TraesCS1D01G006300 chr1D 77.391 345 41 16 4986 5309 363277440 363277112 2.540000e-38 171.0
8 TraesCS1D01G006300 chr1D 79.498 239 22 20 441 670 2889065 2888845 1.540000e-30 145.0
9 TraesCS1D01G006300 chr1D 79.498 239 22 20 730 950 2889354 2889125 1.540000e-30 145.0
10 TraesCS1D01G006300 chr1D 98.750 80 1 0 1272 1351 83123568 83123647 5.540000e-30 143.0
11 TraesCS1D01G006300 chr1A 88.255 2929 322 17 1348 4258 2441258 2438334 0.000000e+00 3483.0
12 TraesCS1D01G006300 chr1A 87.759 2222 237 21 2034 4235 2518057 2520263 0.000000e+00 2564.0
13 TraesCS1D01G006300 chr1A 81.943 1091 124 35 4262 5309 496067463 496066403 0.000000e+00 856.0
14 TraesCS1D01G006300 chr1A 85.780 436 56 2 1348 1777 2490640 2491075 1.740000e-124 457.0
15 TraesCS1D01G006300 chr1A 87.687 268 32 1 1775 2042 2513267 2513533 1.440000e-80 311.0
16 TraesCS1D01G006300 chr1A 83.969 262 31 7 1024 1275 2490372 2490632 1.910000e-59 241.0
17 TraesCS1D01G006300 chr1B 85.778 2250 273 30 2043 4258 1810398 1808162 0.000000e+00 2338.0
18 TraesCS1D01G006300 chr1B 85.941 2205 285 12 2076 4258 1941957 1939756 0.000000e+00 2331.0
19 TraesCS1D01G006300 chr1B 85.039 2306 300 30 1971 4258 712681 714959 0.000000e+00 2305.0
20 TraesCS1D01G006300 chr1B 84.605 2306 305 28 1971 4260 717345 719616 0.000000e+00 2246.0
21 TraesCS1D01G006300 chr1B 83.513 2044 295 20 2253 4258 884154 882115 0.000000e+00 1869.0
22 TraesCS1D01G006300 chr1B 94.965 715 24 4 1 704 710656 711369 0.000000e+00 1110.0
23 TraesCS1D01G006300 chr1B 92.625 678 44 5 1348 2021 1811799 1811124 0.000000e+00 970.0
24 TraesCS1D01G006300 chr1B 87.312 796 96 4 1348 2139 884973 884179 0.000000e+00 905.0
25 TraesCS1D01G006300 chr1B 89.799 647 64 1 1348 1992 1942714 1942068 0.000000e+00 828.0
26 TraesCS1D01G006300 chr1B 88.217 628 67 6 1348 1971 711999 712623 0.000000e+00 743.0
27 TraesCS1D01G006300 chr1B 93.966 464 27 1 1984 2447 2338532 2338994 0.000000e+00 701.0
28 TraesCS1D01G006300 chr1B 84.072 609 49 18 702 1275 711396 711991 1.300000e-150 544.0
29 TraesCS1D01G006300 chr1B 89.948 388 36 3 1586 1971 716901 717287 1.030000e-136 497.0
30 TraesCS1D01G006300 chr1B 84.868 304 41 4 973 1275 1943021 1942722 8.640000e-78 302.0
31 TraesCS1D01G006300 chr1B 80.702 228 14 19 745 951 711118 711336 3.310000e-32 150.0
32 TraesCS1D01G006300 chr5A 92.614 853 48 7 4460 5309 555382696 555381856 0.000000e+00 1212.0
33 TraesCS1D01G006300 chr5A 87.236 948 71 22 4263 5192 604806269 604807184 0.000000e+00 1035.0
34 TraesCS1D01G006300 chr5A 87.838 74 9 0 199 272 17836985 17836912 2.630000e-13 87.9
35 TraesCS1D01G006300 chr6B 88.000 950 65 21 4261 5192 683633409 683634327 0.000000e+00 1077.0
36 TraesCS1D01G006300 chr6B 97.959 49 1 0 5261 5309 683634317 683634365 9.470000e-13 86.1
37 TraesCS1D01G006300 chr4A 87.684 950 68 21 4261 5192 215136148 215135230 0.000000e+00 1061.0
38 TraesCS1D01G006300 chr4A 87.324 710 69 9 4257 4949 694894702 694893997 0.000000e+00 793.0
39 TraesCS1D01G006300 chr4A 77.617 277 37 11 5044 5309 694893931 694893669 1.540000e-30 145.0
40 TraesCS1D01G006300 chr4A 97.959 49 1 0 5261 5309 215135240 215135192 9.470000e-13 86.1
41 TraesCS1D01G006300 chr7B 75.498 1857 393 44 2261 4085 734077572 734075746 0.000000e+00 852.0
42 TraesCS1D01G006300 chr7B 88.095 84 8 2 195 276 354415191 354415274 1.220000e-16 99.0
43 TraesCS1D01G006300 chr2D 87.624 703 70 6 4261 4949 192289813 192290512 0.000000e+00 800.0
44 TraesCS1D01G006300 chr2D 80.637 754 105 34 4569 5309 14435709 14434984 3.620000e-151 545.0
45 TraesCS1D01G006300 chr2D 80.080 251 29 10 5066 5309 192290607 192290843 3.290000e-37 167.0
46 TraesCS1D01G006300 chr2D 97.468 79 2 0 1272 1350 625524338 625524260 9.270000e-28 135.0
47 TraesCS1D01G006300 chr5D 100.000 76 0 0 1272 1347 35163574 35163649 1.990000e-29 141.0
48 TraesCS1D01G006300 chr4D 98.701 77 0 1 1272 1347 438798339 438798415 9.270000e-28 135.0
49 TraesCS1D01G006300 chr4D 97.468 79 1 1 1272 1350 496112108 496112031 3.340000e-27 134.0
50 TraesCS1D01G006300 chr4D 82.895 76 9 3 199 272 438219380 438219453 1.230000e-06 65.8
51 TraesCS1D01G006300 chr7D 97.368 76 1 1 1272 1347 587109735 587109809 1.550000e-25 128.0
52 TraesCS1D01G006300 chr5B 79.058 191 30 8 1358 1543 44867597 44867412 7.220000e-24 122.0
53 TraesCS1D01G006300 chr2A 90.141 71 7 0 195 265 631859128 631859198 5.660000e-15 93.5
54 TraesCS1D01G006300 chr2B 89.041 73 8 0 201 273 705684522 705684594 2.040000e-14 91.6
55 TraesCS1D01G006300 chr3B 86.667 75 10 0 199 273 536459874 536459948 3.410000e-12 84.2
56 TraesCS1D01G006300 chr3B 82.278 79 8 6 194 269 589608885 589608810 4.440000e-06 63.9
57 TraesCS1D01G006300 chr7A 81.707 82 12 3 195 276 40054142 40054220 1.230000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G006300 chr1D 2884486 2889794 5308 True 3364.666667 9804 86.332000 1 5309 3 chr1D.!!$R2 5308
1 TraesCS1D01G006300 chr1D 2716899 2720058 3159 False 1750.500000 3260 85.541000 1024 4235 2 chr1D.!!$F2 3211
2 TraesCS1D01G006300 chr1D 12533100 12535940 2840 False 662.000000 1057 76.209500 1405 4120 2 chr1D.!!$F3 2715
3 TraesCS1D01G006300 chr1D 2477435 2477994 559 True 558.000000 558 84.725000 3699 4258 1 chr1D.!!$R1 559
4 TraesCS1D01G006300 chr1D 363277112 363278144 1032 True 496.000000 821 82.746500 4259 5309 2 chr1D.!!$R3 1050
5 TraesCS1D01G006300 chr1A 2438334 2441258 2924 True 3483.000000 3483 88.255000 1348 4258 1 chr1A.!!$R1 2910
6 TraesCS1D01G006300 chr1A 2518057 2520263 2206 False 2564.000000 2564 87.759000 2034 4235 1 chr1A.!!$F2 2201
7 TraesCS1D01G006300 chr1A 496066403 496067463 1060 True 856.000000 856 81.943000 4262 5309 1 chr1A.!!$R2 1047
8 TraesCS1D01G006300 chr1A 2490372 2491075 703 False 349.000000 457 84.874500 1024 1777 2 chr1A.!!$F3 753
9 TraesCS1D01G006300 chr1B 1808162 1811799 3637 True 1654.000000 2338 89.201500 1348 4258 2 chr1B.!!$R2 2910
10 TraesCS1D01G006300 chr1B 882115 884973 2858 True 1387.000000 1869 85.412500 1348 4258 2 chr1B.!!$R1 2910
11 TraesCS1D01G006300 chr1B 1939756 1943021 3265 True 1153.666667 2331 86.869333 973 4258 3 chr1B.!!$R3 3285
12 TraesCS1D01G006300 chr1B 710656 719616 8960 False 1085.000000 2305 86.792571 1 4260 7 chr1B.!!$F2 4259
13 TraesCS1D01G006300 chr5A 555381856 555382696 840 True 1212.000000 1212 92.614000 4460 5309 1 chr5A.!!$R2 849
14 TraesCS1D01G006300 chr5A 604806269 604807184 915 False 1035.000000 1035 87.236000 4263 5192 1 chr5A.!!$F1 929
15 TraesCS1D01G006300 chr6B 683633409 683634365 956 False 581.550000 1077 92.979500 4261 5309 2 chr6B.!!$F1 1048
16 TraesCS1D01G006300 chr4A 215135192 215136148 956 True 573.550000 1061 92.821500 4261 5309 2 chr4A.!!$R1 1048
17 TraesCS1D01G006300 chr4A 694893669 694894702 1033 True 469.000000 793 82.470500 4257 5309 2 chr4A.!!$R2 1052
18 TraesCS1D01G006300 chr7B 734075746 734077572 1826 True 852.000000 852 75.498000 2261 4085 1 chr7B.!!$R1 1824
19 TraesCS1D01G006300 chr2D 14434984 14435709 725 True 545.000000 545 80.637000 4569 5309 1 chr2D.!!$R1 740
20 TraesCS1D01G006300 chr2D 192289813 192290843 1030 False 483.500000 800 83.852000 4261 5309 2 chr2D.!!$F1 1048

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
860 901 0.038251 GACATCGTGAGGTCACTGCA 60.038 55.0 9.57 0.0 44.34 4.41 F
1346 1431 0.107017 AATTCCTGGATCCGCCACTG 60.107 55.0 7.39 0.0 43.33 3.66 F
1592 1677 0.170339 GCGGACACCAAAGGTAATGC 59.830 55.0 0.00 0.0 32.11 3.56 F
1750 1841 1.243902 TTGTTGGATTTGGCGGACTC 58.756 50.0 0.00 0.0 0.00 3.36 F
2381 3424 1.537814 CCACCCGCATAGCCGGTATA 61.538 60.0 1.90 0.0 46.71 1.47 F
3687 4785 1.144691 TGTCAGTTGGGATGGTTGGA 58.855 50.0 0.00 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1916 1.071385 GCCATGTCAGGATTCCGAGAT 59.929 52.381 0.00 0.0 0.00 2.75 R
3044 4088 0.108138 ATCTACGACCCTTGCTGTGC 60.108 55.000 0.00 0.0 0.00 4.57 R
3433 4495 0.179156 CGCTGAATCGGCTGCATTTT 60.179 50.000 12.66 0.0 32.89 1.82 R
3451 4513 0.461339 CCCGATCCCAACTGGTAACG 60.461 60.000 0.00 0.0 42.51 3.18 R
4034 9789 0.104304 GGTCACCGCCGACAATATCT 59.896 55.000 5.03 0.0 37.66 1.98 R
4589 10369 1.916777 CTGGAAGGTGTACGGGGGT 60.917 63.158 0.00 0.0 0.00 4.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 5.711506 TGAACTACAAATGTGCCTCATGATT 59.288 36.000 0.00 0.00 36.81 2.57
105 106 7.392953 TGAACTACAAATGTGCCTCATGATTAA 59.607 33.333 0.00 0.00 36.81 1.40
111 112 7.093640 ACAAATGTGCCTCATGATTAACTTGAT 60.094 33.333 0.00 0.00 36.81 2.57
243 244 6.847421 ACAAGGTCGTAGTAAGGTTAAGAT 57.153 37.500 0.00 0.00 0.00 2.40
329 330 7.502696 TCTTTAGTGTTAACTCACCAAGCTTA 58.497 34.615 7.22 0.00 38.91 3.09
375 380 9.725019 AATTCATATCATATACACACACCGAAT 57.275 29.630 0.00 0.00 0.00 3.34
381 386 6.578023 TCATATACACACACCGAATCATGAA 58.422 36.000 0.00 0.00 0.00 2.57
410 415 4.002982 TCACTGCATCATCAAGTTACACC 58.997 43.478 0.00 0.00 0.00 4.16
438 443 5.877012 ACGTGAAGAAGAATCACTGCATAAT 59.123 36.000 5.28 0.00 43.93 1.28
519 528 0.099436 GGCGCCTCTAACAAAGCATG 59.901 55.000 22.15 0.00 0.00 4.06
593 602 2.033141 GGGCTCACTGCAGCAAGA 59.967 61.111 15.27 8.79 45.15 3.02
596 605 1.575576 GGCTCACTGCAGCAAGACAG 61.576 60.000 15.27 1.76 45.15 3.51
634 646 2.034879 GGGGTCACTCACGCACATG 61.035 63.158 0.00 0.00 39.79 3.21
635 647 2.034879 GGGTCACTCACGCACATGG 61.035 63.158 0.00 0.00 37.88 3.66
637 649 1.291877 GGTCACTCACGCACATGGAC 61.292 60.000 0.00 0.00 0.00 4.02
670 682 1.210478 ACCACCATCCATCTGTAGCAC 59.790 52.381 0.00 0.00 0.00 4.40
704 716 4.262549 CCAGCTCTATCATTAGAAGCAGCT 60.263 45.833 0.00 0.00 34.37 4.24
706 718 4.834496 AGCTCTATCATTAGAAGCAGCTCT 59.166 41.667 0.00 0.00 34.06 4.09
751 792 4.749245 AAAACAGAGCTTTACATGACCG 57.251 40.909 0.00 0.00 0.00 4.79
752 793 3.402628 AACAGAGCTTTACATGACCGT 57.597 42.857 0.00 0.00 0.00 4.83
753 794 2.960819 ACAGAGCTTTACATGACCGTC 58.039 47.619 0.00 0.00 0.00 4.79
754 795 2.271800 CAGAGCTTTACATGACCGTCC 58.728 52.381 0.00 0.00 0.00 4.79
756 797 2.093973 AGAGCTTTACATGACCGTCCAG 60.094 50.000 0.00 0.00 0.00 3.86
757 798 1.899814 AGCTTTACATGACCGTCCAGA 59.100 47.619 0.00 0.00 0.00 3.86
758 799 2.093973 AGCTTTACATGACCGTCCAGAG 60.094 50.000 0.00 0.00 0.00 3.35
759 800 2.094182 GCTTTACATGACCGTCCAGAGA 60.094 50.000 0.00 0.00 0.00 3.10
760 801 3.775202 CTTTACATGACCGTCCAGAGAG 58.225 50.000 0.00 0.00 0.00 3.20
761 802 1.103803 TACATGACCGTCCAGAGAGC 58.896 55.000 0.00 0.00 0.00 4.09
762 803 0.900182 ACATGACCGTCCAGAGAGCA 60.900 55.000 0.00 0.00 0.00 4.26
763 804 0.459237 CATGACCGTCCAGAGAGCAC 60.459 60.000 0.00 0.00 0.00 4.40
764 805 1.938657 ATGACCGTCCAGAGAGCACG 61.939 60.000 0.00 0.00 0.00 5.34
766 807 4.135153 CCGTCCAGAGAGCACGGG 62.135 72.222 1.69 0.00 39.96 5.28
767 808 4.803426 CGTCCAGAGAGCACGGGC 62.803 72.222 0.00 0.00 41.61 6.13
768 809 4.459089 GTCCAGAGAGCACGGGCC 62.459 72.222 5.73 0.00 42.56 5.80
791 832 3.282885 CTCCAAATCTTACCTCCTTGGC 58.717 50.000 0.00 0.00 40.22 4.52
793 834 2.755103 CCAAATCTTACCTCCTTGGCAC 59.245 50.000 0.00 0.00 40.22 5.01
828 869 2.124570 ATGCCAGACATCGTGGGC 60.125 61.111 0.00 0.00 46.58 5.36
856 897 1.071605 GCAAGACATCGTGAGGTCAC 58.928 55.000 15.96 0.00 43.84 3.67
858 899 2.332104 CAAGACATCGTGAGGTCACTG 58.668 52.381 15.96 9.23 43.84 3.66
859 900 0.244994 AGACATCGTGAGGTCACTGC 59.755 55.000 15.96 0.00 43.84 4.40
860 901 0.038251 GACATCGTGAGGTCACTGCA 60.038 55.000 9.57 0.00 44.34 4.41
862 903 1.079543 ATCGTGAGGTCACTGCAGC 60.080 57.895 15.27 0.00 44.34 5.25
864 905 1.595109 CGTGAGGTCACTGCAGCAA 60.595 57.895 15.27 0.00 44.34 3.91
865 906 1.835483 CGTGAGGTCACTGCAGCAAC 61.835 60.000 15.27 12.11 44.34 4.17
866 907 0.815213 GTGAGGTCACTGCAGCAACA 60.815 55.000 15.27 3.13 43.25 3.33
867 908 0.815213 TGAGGTCACTGCAGCAACAC 60.815 55.000 15.27 10.37 0.00 3.32
868 909 0.815213 GAGGTCACTGCAGCAACACA 60.815 55.000 15.27 0.00 0.00 3.72
869 910 0.179009 AGGTCACTGCAGCAACACAT 60.179 50.000 15.27 0.00 0.00 3.21
870 911 0.239347 GGTCACTGCAGCAACACATC 59.761 55.000 15.27 0.00 0.00 3.06
871 912 1.233019 GTCACTGCAGCAACACATCT 58.767 50.000 15.27 0.00 0.00 2.90
872 913 2.416747 GTCACTGCAGCAACACATCTA 58.583 47.619 15.27 0.00 0.00 1.98
873 914 3.005554 GTCACTGCAGCAACACATCTAT 58.994 45.455 15.27 0.00 0.00 1.98
874 915 3.438087 GTCACTGCAGCAACACATCTATT 59.562 43.478 15.27 0.00 0.00 1.73
876 917 5.295292 GTCACTGCAGCAACACATCTATTAT 59.705 40.000 15.27 0.00 0.00 1.28
877 918 5.295045 TCACTGCAGCAACACATCTATTATG 59.705 40.000 15.27 0.00 0.00 1.90
879 920 3.946558 TGCAGCAACACATCTATTATGCA 59.053 39.130 0.00 0.00 38.70 3.96
880 921 4.398673 TGCAGCAACACATCTATTATGCAA 59.601 37.500 0.00 0.00 38.13 4.08
881 922 5.068067 TGCAGCAACACATCTATTATGCAAT 59.932 36.000 0.00 0.00 38.13 3.56
882 923 5.981315 GCAGCAACACATCTATTATGCAATT 59.019 36.000 0.00 0.00 36.30 2.32
884 925 7.648908 GCAGCAACACATCTATTATGCAATTTA 59.351 33.333 0.00 0.00 36.30 1.40
885 926 9.518906 CAGCAACACATCTATTATGCAATTTAA 57.481 29.630 0.00 0.00 36.30 1.52
886 927 9.740239 AGCAACACATCTATTATGCAATTTAAG 57.260 29.630 0.00 0.00 36.30 1.85
887 928 8.971321 GCAACACATCTATTATGCAATTTAAGG 58.029 33.333 0.00 0.00 34.10 2.69
890 931 8.632679 ACACATCTATTATGCAATTTAAGGTGG 58.367 33.333 0.00 0.00 0.00 4.61
891 932 8.849168 CACATCTATTATGCAATTTAAGGTGGA 58.151 33.333 0.00 0.00 0.00 4.02
892 933 9.071276 ACATCTATTATGCAATTTAAGGTGGAG 57.929 33.333 0.00 0.00 0.00 3.86
893 934 8.517878 CATCTATTATGCAATTTAAGGTGGAGG 58.482 37.037 0.00 0.00 0.00 4.30
894 935 7.004086 TCTATTATGCAATTTAAGGTGGAGGG 58.996 38.462 0.00 0.00 0.00 4.30
895 936 2.230130 TGCAATTTAAGGTGGAGGGG 57.770 50.000 0.00 0.00 0.00 4.79
898 939 2.556559 GCAATTTAAGGTGGAGGGGTCA 60.557 50.000 0.00 0.00 0.00 4.02
899 940 3.089284 CAATTTAAGGTGGAGGGGTCAC 58.911 50.000 0.00 0.00 34.61 3.67
994 1053 1.821061 AACCCAGCGTCTCCTCTGTG 61.821 60.000 0.00 0.00 0.00 3.66
1038 1111 0.469331 TCGTCACCACCAACTCCTCT 60.469 55.000 0.00 0.00 0.00 3.69
1041 1114 0.764369 TCACCACCAACTCCTCTGCT 60.764 55.000 0.00 0.00 0.00 4.24
1065 1138 2.026905 GCAAGAAAACACACCCCTCCA 61.027 52.381 0.00 0.00 0.00 3.86
1068 1144 1.029681 GAAAACACACCCCTCCACAC 58.970 55.000 0.00 0.00 0.00 3.82
1096 1181 2.512896 GAAGCCGCCATGATCCCT 59.487 61.111 0.00 0.00 0.00 4.20
1147 1232 2.094649 GGACGAGTACAACCTGGAGAAG 60.095 54.545 0.00 0.00 0.00 2.85
1217 1302 0.800683 CGCCGTTCTACGCAAGATCA 60.801 55.000 0.00 0.00 40.91 2.92
1247 1332 2.383527 GCCGAGCTGTTTGACGAGG 61.384 63.158 0.00 0.00 0.00 4.63
1275 1360 1.118356 ATTTGGGCGGGCAAAGTGAA 61.118 50.000 3.27 0.00 0.00 3.18
1276 1361 2.022240 TTTGGGCGGGCAAAGTGAAC 62.022 55.000 3.27 0.00 0.00 3.18
1279 1364 2.548295 GGCGGGCAAAGTGAACGAA 61.548 57.895 0.00 0.00 0.00 3.85
1280 1365 1.579429 GCGGGCAAAGTGAACGAAT 59.421 52.632 0.00 0.00 0.00 3.34
1282 1367 1.685302 CGGGCAAAGTGAACGAATTG 58.315 50.000 0.00 0.00 0.00 2.32
1283 1368 1.665735 CGGGCAAAGTGAACGAATTGG 60.666 52.381 0.00 0.00 0.00 3.16
1284 1369 1.418373 GGCAAAGTGAACGAATTGGC 58.582 50.000 0.00 0.00 40.40 4.52
1285 1370 1.000274 GGCAAAGTGAACGAATTGGCT 60.000 47.619 12.52 0.00 42.88 4.75
1286 1371 2.319472 GCAAAGTGAACGAATTGGCTC 58.681 47.619 0.00 0.00 0.00 4.70
1287 1372 2.922335 GCAAAGTGAACGAATTGGCTCC 60.922 50.000 0.00 0.00 0.00 4.70
1288 1373 2.554032 CAAAGTGAACGAATTGGCTCCT 59.446 45.455 0.00 0.00 0.00 3.69
1289 1374 2.100605 AGTGAACGAATTGGCTCCTC 57.899 50.000 0.00 0.00 0.00 3.71
1290 1375 1.625818 AGTGAACGAATTGGCTCCTCT 59.374 47.619 0.00 0.00 0.00 3.69
1291 1376 1.734465 GTGAACGAATTGGCTCCTCTG 59.266 52.381 0.00 0.00 0.00 3.35
1292 1377 1.347707 TGAACGAATTGGCTCCTCTGT 59.652 47.619 0.00 0.00 0.00 3.41
1293 1378 2.224523 TGAACGAATTGGCTCCTCTGTT 60.225 45.455 0.00 0.00 0.00 3.16
1294 1379 3.007506 TGAACGAATTGGCTCCTCTGTTA 59.992 43.478 0.00 0.00 0.00 2.41
1295 1380 3.252974 ACGAATTGGCTCCTCTGTTAG 57.747 47.619 0.00 0.00 0.00 2.34
1296 1381 2.567615 ACGAATTGGCTCCTCTGTTAGT 59.432 45.455 0.00 0.00 0.00 2.24
1297 1382 2.932614 CGAATTGGCTCCTCTGTTAGTG 59.067 50.000 0.00 0.00 0.00 2.74
1298 1383 3.617531 CGAATTGGCTCCTCTGTTAGTGT 60.618 47.826 0.00 0.00 0.00 3.55
1299 1384 2.839486 TTGGCTCCTCTGTTAGTGTG 57.161 50.000 0.00 0.00 0.00 3.82
1300 1385 2.009681 TGGCTCCTCTGTTAGTGTGA 57.990 50.000 0.00 0.00 0.00 3.58
1301 1386 2.325484 TGGCTCCTCTGTTAGTGTGAA 58.675 47.619 0.00 0.00 0.00 3.18
1302 1387 2.703536 TGGCTCCTCTGTTAGTGTGAAA 59.296 45.455 0.00 0.00 0.00 2.69
1303 1388 3.135712 TGGCTCCTCTGTTAGTGTGAAAA 59.864 43.478 0.00 0.00 0.00 2.29
1304 1389 4.134563 GGCTCCTCTGTTAGTGTGAAAAA 58.865 43.478 0.00 0.00 0.00 1.94
1332 1417 8.846943 AATTTGAACACCCAATTCTAAATTCC 57.153 30.769 0.00 0.00 30.10 3.01
1333 1418 7.610580 TTTGAACACCCAATTCTAAATTCCT 57.389 32.000 0.00 0.00 0.00 3.36
1334 1419 6.588719 TGAACACCCAATTCTAAATTCCTG 57.411 37.500 0.00 0.00 0.00 3.86
1335 1420 5.480073 TGAACACCCAATTCTAAATTCCTGG 59.520 40.000 0.00 0.00 0.00 4.45
1336 1421 5.269554 ACACCCAATTCTAAATTCCTGGA 57.730 39.130 0.00 0.00 0.00 3.86
1337 1422 5.842339 ACACCCAATTCTAAATTCCTGGAT 58.158 37.500 0.00 0.00 0.00 3.41
1338 1423 5.893824 ACACCCAATTCTAAATTCCTGGATC 59.106 40.000 0.00 0.00 0.00 3.36
1339 1424 5.302823 CACCCAATTCTAAATTCCTGGATCC 59.697 44.000 4.20 4.20 0.00 3.36
1340 1425 4.520492 CCCAATTCTAAATTCCTGGATCCG 59.480 45.833 7.39 1.76 0.00 4.18
1341 1426 4.022849 CCAATTCTAAATTCCTGGATCCGC 60.023 45.833 7.39 0.00 0.00 5.54
1342 1427 2.930826 TCTAAATTCCTGGATCCGCC 57.069 50.000 7.39 0.00 37.10 6.13
1343 1428 2.123589 TCTAAATTCCTGGATCCGCCA 58.876 47.619 7.39 0.00 46.96 5.69
1344 1429 2.158813 TCTAAATTCCTGGATCCGCCAC 60.159 50.000 7.39 0.00 43.33 5.01
1345 1430 0.625849 AAATTCCTGGATCCGCCACT 59.374 50.000 7.39 0.00 43.33 4.00
1346 1431 0.107017 AATTCCTGGATCCGCCACTG 60.107 55.000 7.39 0.00 43.33 3.66
1408 1493 1.600107 GTGGAGGACGTTGGCCATA 59.400 57.895 6.09 0.00 32.26 2.74
1498 1583 2.839228 AGGGTAAGGCTCTTCATCAGT 58.161 47.619 0.00 0.00 0.00 3.41
1592 1677 0.170339 GCGGACACCAAAGGTAATGC 59.830 55.000 0.00 0.00 32.11 3.56
1750 1841 1.243902 TTGTTGGATTTGGCGGACTC 58.756 50.000 0.00 0.00 0.00 3.36
1825 1916 7.908827 TGATAATGTAGCTTTTGTTTCCGTA 57.091 32.000 0.00 0.00 0.00 4.02
1855 1946 4.314522 TCCTGACATGGCCAAGATTTTA 57.685 40.909 16.33 0.00 0.00 1.52
1973 2121 7.038302 TGTTTCTTCAGGACAAGAGGTATGTAT 60.038 37.037 0.00 0.00 33.85 2.29
1986 2242 6.595682 AGAGGTATGTATGTAGCAGCAAATT 58.404 36.000 0.00 0.00 0.00 1.82
2046 3010 3.867493 GCTAGTAAATACCGTGTCCCAAC 59.133 47.826 0.00 0.00 0.00 3.77
2098 3103 5.048713 GCGCTGATATTAGGCCTTACATTTT 60.049 40.000 12.58 0.00 0.00 1.82
2111 3116 6.037062 GGCCTTACATTTTTGTTTCATATGCC 59.963 38.462 0.00 0.00 0.00 4.40
2117 3122 7.669427 ACATTTTTGTTTCATATGCCTCTTCA 58.331 30.769 0.00 0.00 0.00 3.02
2243 3280 9.840427 CCTAGTTATGTTGGTTGATTTGTAAAG 57.160 33.333 0.00 0.00 0.00 1.85
2251 3288 6.132791 TGGTTGATTTGTAAAGTAACGCAA 57.867 33.333 0.00 0.00 0.00 4.85
2328 3371 6.065374 TGGGAACTTATTAAGTGTGCTTTCA 58.935 36.000 9.78 0.93 41.91 2.69
2376 3419 2.029073 CTACCACCCGCATAGCCG 59.971 66.667 0.00 0.00 0.00 5.52
2381 3424 1.537814 CCACCCGCATAGCCGGTATA 61.538 60.000 1.90 0.00 46.71 1.47
2387 3430 3.321111 CCCGCATAGCCGGTATATCTAAT 59.679 47.826 1.90 0.00 46.71 1.73
2389 3432 4.202121 CCGCATAGCCGGTATATCTAATGT 60.202 45.833 1.90 0.00 43.24 2.71
2450 3493 3.448934 ACCACTTCCTGATGATGACTCT 58.551 45.455 0.00 0.00 0.00 3.24
2511 3554 1.905215 AGTGTCCTGATGAGTTGGAGG 59.095 52.381 0.00 0.00 0.00 4.30
2573 3616 4.383173 CACTAGCCATCATCACTATTGCA 58.617 43.478 0.00 0.00 0.00 4.08
2588 3631 8.142994 TCACTATTGCAAGTATTTTAGCTAGC 57.857 34.615 6.62 6.62 0.00 3.42
2589 3632 7.042725 TCACTATTGCAAGTATTTTAGCTAGCG 60.043 37.037 9.55 0.00 0.00 4.26
2596 3639 4.884247 AGTATTTTAGCTAGCGATGGTCC 58.116 43.478 9.55 0.00 0.00 4.46
2601 3644 2.294449 AGCTAGCGATGGTCCAGATA 57.706 50.000 9.55 0.00 0.00 1.98
2609 3652 3.743396 GCGATGGTCCAGATAAACAGATC 59.257 47.826 0.00 0.00 0.00 2.75
2671 3714 2.036387 TCGTGGACTTGAAGAAGGTGA 58.964 47.619 0.00 0.00 32.95 4.02
2704 3747 5.858381 GGACATGCAGAGAATATTGTCCTA 58.142 41.667 19.79 0.00 40.78 2.94
2949 3993 2.215196 GTAAGGTGGAAACTTGTCGCA 58.785 47.619 0.00 0.00 0.00 5.10
2970 4014 4.560716 GCATGCATGATATGGTGCTTGATT 60.561 41.667 30.64 0.00 44.54 2.57
2987 4031 5.621197 TTGATTTGTTATGTTCCCTGTCG 57.379 39.130 0.00 0.00 0.00 4.35
3044 4088 9.032420 GGTACTCAATAGAGAAAACCTATTTCG 57.968 37.037 0.00 0.00 44.98 3.46
3059 4103 2.933878 TTTCGCACAGCAAGGGTCGT 62.934 55.000 0.00 0.00 0.00 4.34
3065 4109 2.002586 CACAGCAAGGGTCGTAGATTG 58.997 52.381 0.00 0.00 40.67 2.67
3122 4166 1.583054 GGGTCGATGCCACAAGTATC 58.417 55.000 0.00 0.00 34.47 2.24
3148 4192 4.649674 ACAAGTGAGGTCTGTTGTTCTCTA 59.350 41.667 0.00 0.00 28.62 2.43
3193 4237 6.475504 TCCAGACTATTTCATGCTTTCAAGA 58.524 36.000 0.00 0.00 0.00 3.02
3256 4300 6.543465 AGAAATCGCCACAATATTGATCTCAA 59.457 34.615 22.16 3.47 40.51 3.02
3384 4428 6.456181 CGACTTAGCAGAAAATGGATCAACTC 60.456 42.308 0.00 0.00 0.00 3.01
3399 4461 4.890158 TCAACTCTAGCAGTGATTCCAA 57.110 40.909 0.00 0.00 34.56 3.53
3433 4495 3.615056 CGTCTAACACGTTTGATATGCCA 59.385 43.478 0.00 0.00 44.07 4.92
3451 4513 1.274596 CAAAATGCAGCCGATTCAGC 58.725 50.000 0.00 0.00 0.00 4.26
3473 4538 1.200519 TACCAGTTGGGATCGGGAAG 58.799 55.000 2.79 0.00 41.15 3.46
3501 4566 5.105146 ACGTCATTAGAAGAGCTGAAAGGAT 60.105 40.000 0.00 0.00 0.00 3.24
3504 4569 7.043059 CGTCATTAGAAGAGCTGAAAGGATTAC 60.043 40.741 0.00 0.00 0.00 1.89
3586 4681 1.756538 TGGAAGCGATGAGAGCATGTA 59.243 47.619 0.00 0.00 34.11 2.29
3674 4772 2.355513 GGATGCAAGGTCTGATGTCAGT 60.356 50.000 9.65 0.00 44.12 3.41
3687 4785 1.144691 TGTCAGTTGGGATGGTTGGA 58.855 50.000 0.00 0.00 0.00 3.53
3760 9511 4.601406 TGCCTAGGTGGGTTAATTCATT 57.399 40.909 11.31 0.00 36.00 2.57
3797 9548 3.519107 TCTCCTCCATGCATGTTTCAGTA 59.481 43.478 24.58 2.61 0.00 2.74
3809 9561 2.621526 TGTTTCAGTAGACAGAGTGCGA 59.378 45.455 0.00 0.00 0.00 5.10
3943 9698 4.019411 TGCATTCCCATGTTTGAGAGAGTA 60.019 41.667 0.00 0.00 32.28 2.59
3977 9732 5.314573 TGGTTTTATCATGGGGCCATCTATA 59.685 40.000 4.39 0.00 33.90 1.31
4034 9789 1.301716 GTTCTCAGCCCAAGCGTCA 60.302 57.895 0.00 0.00 46.67 4.35
4086 9843 1.306568 GAGCACCTCCCTTCCCTCT 60.307 63.158 0.00 0.00 0.00 3.69
4150 9907 3.840666 TCAGATAAGTGCAAGGAGGAAGT 59.159 43.478 0.00 0.00 0.00 3.01
4200 9957 1.453745 CATCCCAACCATCCCACCG 60.454 63.158 0.00 0.00 0.00 4.94
4216 9982 0.388907 ACCGTTCGTACCATTCGTGG 60.389 55.000 0.00 0.00 0.00 4.94
4297 10063 0.608130 TCCGCCTGCTAATATCGCAT 59.392 50.000 0.72 0.00 36.70 4.73
4302 10068 3.679980 CGCCTGCTAATATCGCATTTAGT 59.320 43.478 0.72 0.00 36.70 2.24
4315 10081 4.941263 TCGCATTTAGTATCCTGCAAAACT 59.059 37.500 0.00 0.00 34.29 2.66
4320 10086 0.179163 GTATCCTGCAAAACTGCCGC 60.179 55.000 0.00 0.00 0.00 6.53
4404 10171 0.672889 TGTCGTTACCCGTGTTGCTA 59.327 50.000 0.00 0.00 37.94 3.49
4467 10247 2.835431 CGAGGTCAGGGCGAGGAT 60.835 66.667 0.00 0.00 0.00 3.24
4779 10559 2.106566 GATCCTCCTGTCTTCTCTGCA 58.893 52.381 0.00 0.00 0.00 4.41
4813 10593 1.062488 AAGCTCCTCACAGGGTTGGT 61.062 55.000 0.00 0.00 35.59 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 3.815401 GAGGCACATTTGTAGTTCACACT 59.185 43.478 0.00 0.00 36.69 3.55
76 77 3.563808 TGAGGCACATTTGTAGTTCACAC 59.436 43.478 0.00 0.00 36.69 3.82
105 106 9.953565 ATGAAATTTCAAATCCATCAATCAAGT 57.046 25.926 23.91 0.00 41.13 3.16
111 112 9.434420 GGTGTAATGAAATTTCAAATCCATCAA 57.566 29.630 23.91 0.00 41.13 2.57
167 168 9.973450 GAGTGAGTACATGATATGAATTACACT 57.027 33.333 0.00 0.00 35.28 3.55
243 244 4.533311 ACTCCCTTCGTCCCAAAATAAGTA 59.467 41.667 0.00 0.00 0.00 2.24
304 305 5.925509 AGCTTGGTGAGTTAACACTAAAGA 58.074 37.500 8.61 0.00 39.82 2.52
375 380 6.578163 TGATGCAGTGATTTTTCTTCATGA 57.422 33.333 0.00 0.00 0.00 3.07
381 386 6.585695 ACTTGATGATGCAGTGATTTTTCT 57.414 33.333 0.00 0.00 0.00 2.52
410 415 2.476619 AGTGATTCTTCTTCACGTTGCG 59.523 45.455 0.00 0.00 46.39 4.85
519 528 2.523412 ATGCTGGCATGGCATCCC 60.523 61.111 23.59 14.16 45.85 3.85
605 614 2.571653 TGAGTGACCCCTCCACTAATTG 59.428 50.000 0.00 0.00 44.14 2.32
634 646 1.521681 GGTATGCAGCAGTCCGTCC 60.522 63.158 0.00 0.00 0.00 4.79
635 647 1.084370 GTGGTATGCAGCAGTCCGTC 61.084 60.000 0.00 0.30 31.49 4.79
637 649 1.815421 GGTGGTATGCAGCAGTCCG 60.815 63.158 0.00 0.00 31.49 4.79
670 682 5.287674 TGATAGAGCTGGAGAAAATGAGG 57.712 43.478 0.00 0.00 0.00 3.86
704 716 3.897141 TTTACACATCGCCATGGTAGA 57.103 42.857 14.67 13.79 33.82 2.59
706 718 4.328536 AGTTTTTACACATCGCCATGGTA 58.671 39.130 14.67 2.05 33.82 3.25
751 792 4.459089 GGCCCGTGCTCTCTGGAC 62.459 72.222 0.00 0.00 37.74 4.02
761 802 3.508840 GATTTGGAGCGGCCCGTG 61.509 66.667 4.45 0.00 34.97 4.94
762 803 1.906105 TAAGATTTGGAGCGGCCCGT 61.906 55.000 4.45 0.00 34.97 5.28
763 804 1.153249 TAAGATTTGGAGCGGCCCG 60.153 57.895 0.00 0.00 34.97 6.13
764 805 1.101635 GGTAAGATTTGGAGCGGCCC 61.102 60.000 0.00 0.00 34.97 5.80
765 806 0.107165 AGGTAAGATTTGGAGCGGCC 60.107 55.000 0.00 0.00 37.10 6.13
766 807 1.300481 GAGGTAAGATTTGGAGCGGC 58.700 55.000 0.00 0.00 0.00 6.53
767 808 1.486726 AGGAGGTAAGATTTGGAGCGG 59.513 52.381 0.00 0.00 0.00 5.52
768 809 2.939103 CAAGGAGGTAAGATTTGGAGCG 59.061 50.000 0.00 0.00 0.00 5.03
791 832 2.972625 TCCGATGCTTTGTTAGAGGTG 58.027 47.619 0.00 0.00 0.00 4.00
823 864 2.280797 TTGCAGTGTCGAGCCCAC 60.281 61.111 0.00 0.00 0.00 4.61
828 869 0.987715 CGATGTCTTGCAGTGTCGAG 59.012 55.000 0.00 0.00 0.00 4.04
856 897 4.035909 TGCATAATAGATGTGTTGCTGCAG 59.964 41.667 10.11 10.11 33.58 4.41
858 899 4.556942 TGCATAATAGATGTGTTGCTGC 57.443 40.909 0.00 0.00 0.00 5.25
859 900 7.997107 AAATTGCATAATAGATGTGTTGCTG 57.003 32.000 0.00 0.00 0.00 4.41
860 901 9.740239 CTTAAATTGCATAATAGATGTGTTGCT 57.260 29.630 0.00 0.00 0.00 3.91
864 905 8.632679 CCACCTTAAATTGCATAATAGATGTGT 58.367 33.333 0.00 0.00 0.00 3.72
865 906 8.849168 TCCACCTTAAATTGCATAATAGATGTG 58.151 33.333 0.00 0.00 0.00 3.21
866 907 8.995027 TCCACCTTAAATTGCATAATAGATGT 57.005 30.769 0.00 0.00 0.00 3.06
867 908 8.517878 CCTCCACCTTAAATTGCATAATAGATG 58.482 37.037 0.00 0.00 0.00 2.90
868 909 7.671398 CCCTCCACCTTAAATTGCATAATAGAT 59.329 37.037 0.00 0.00 0.00 1.98
869 910 7.004086 CCCTCCACCTTAAATTGCATAATAGA 58.996 38.462 0.00 0.00 0.00 1.98
870 911 6.209391 CCCCTCCACCTTAAATTGCATAATAG 59.791 42.308 0.00 0.00 0.00 1.73
871 912 6.074648 CCCCTCCACCTTAAATTGCATAATA 58.925 40.000 0.00 0.00 0.00 0.98
872 913 4.901250 CCCCTCCACCTTAAATTGCATAAT 59.099 41.667 0.00 0.00 0.00 1.28
873 914 4.264623 ACCCCTCCACCTTAAATTGCATAA 60.265 41.667 0.00 0.00 0.00 1.90
874 915 3.270960 ACCCCTCCACCTTAAATTGCATA 59.729 43.478 0.00 0.00 0.00 3.14
876 917 1.431243 ACCCCTCCACCTTAAATTGCA 59.569 47.619 0.00 0.00 0.00 4.08
877 918 2.100197 GACCCCTCCACCTTAAATTGC 58.900 52.381 0.00 0.00 0.00 3.56
879 920 2.993863 AGTGACCCCTCCACCTTAAATT 59.006 45.455 0.00 0.00 35.23 1.82
880 921 2.576648 GAGTGACCCCTCCACCTTAAAT 59.423 50.000 0.00 0.00 35.23 1.40
881 922 1.982958 GAGTGACCCCTCCACCTTAAA 59.017 52.381 0.00 0.00 35.23 1.52
882 923 1.652947 GAGTGACCCCTCCACCTTAA 58.347 55.000 0.00 0.00 35.23 1.85
884 925 1.913762 CGAGTGACCCCTCCACCTT 60.914 63.158 0.00 0.00 35.23 3.50
885 926 2.283966 CGAGTGACCCCTCCACCT 60.284 66.667 0.00 0.00 35.23 4.00
886 927 4.083862 GCGAGTGACCCCTCCACC 62.084 72.222 0.00 0.00 35.23 4.61
887 928 4.083862 GGCGAGTGACCCCTCCAC 62.084 72.222 0.00 0.00 34.89 4.02
890 931 4.083862 GTGGGCGAGTGACCCCTC 62.084 72.222 0.00 0.00 46.01 4.30
891 932 4.640690 AGTGGGCGAGTGACCCCT 62.641 66.667 0.00 0.00 46.01 4.79
892 933 4.083862 GAGTGGGCGAGTGACCCC 62.084 72.222 0.00 0.00 46.01 4.95
893 934 3.311110 TGAGTGGGCGAGTGACCC 61.311 66.667 0.00 0.00 46.01 4.46
895 936 2.430921 CGTGAGTGGGCGAGTGAC 60.431 66.667 0.00 0.00 0.00 3.67
898 939 4.664677 GTGCGTGAGTGGGCGAGT 62.665 66.667 0.00 0.00 0.00 4.18
899 940 3.939837 ATGTGCGTGAGTGGGCGAG 62.940 63.158 0.00 0.00 0.00 5.03
994 1053 4.376146 GGTTGATTGATAGAGCTGGAGAC 58.624 47.826 0.00 0.00 0.00 3.36
1041 1114 2.092103 AGGGGTGTGTTTTCTTGCTGTA 60.092 45.455 0.00 0.00 0.00 2.74
1065 1138 1.607467 GCTTCCATGGCTTGGGTGT 60.607 57.895 18.35 0.00 46.45 4.16
1068 1144 3.142838 CGGCTTCCATGGCTTGGG 61.143 66.667 18.35 5.56 46.45 4.12
1081 1157 1.454479 CAAAGGGATCATGGCGGCT 60.454 57.895 11.43 0.00 0.00 5.52
1096 1181 1.078709 CGCCGAGCTTCTTGATCAAA 58.921 50.000 9.88 0.00 0.00 2.69
1184 1269 2.242572 CGGCGTGCATCATCTCCAG 61.243 63.158 0.00 0.00 0.00 3.86
1236 1321 3.143010 AGGACCTCCTCGTCAAACA 57.857 52.632 0.00 0.00 44.77 2.83
1247 1332 1.452108 CCGCCCAAATGAGGACCTC 60.452 63.158 15.13 15.13 0.00 3.85
1258 1343 2.123683 TTCACTTTGCCCGCCCAA 60.124 55.556 0.00 0.00 0.00 4.12
1275 1360 2.567615 ACTAACAGAGGAGCCAATTCGT 59.432 45.455 0.00 0.00 0.00 3.85
1276 1361 2.932614 CACTAACAGAGGAGCCAATTCG 59.067 50.000 0.00 0.00 0.00 3.34
1279 1364 2.906389 TCACACTAACAGAGGAGCCAAT 59.094 45.455 0.00 0.00 0.00 3.16
1280 1365 2.325484 TCACACTAACAGAGGAGCCAA 58.675 47.619 0.00 0.00 0.00 4.52
1282 1367 3.402628 TTTCACACTAACAGAGGAGCC 57.597 47.619 0.00 0.00 0.00 4.70
1306 1391 9.283768 GGAATTTAGAATTGGGTGTTCAAATTT 57.716 29.630 0.00 0.00 32.73 1.82
1307 1392 8.659527 AGGAATTTAGAATTGGGTGTTCAAATT 58.340 29.630 0.00 0.00 33.81 1.82
1308 1393 8.096414 CAGGAATTTAGAATTGGGTGTTCAAAT 58.904 33.333 0.00 0.00 0.00 2.32
1309 1394 7.441017 CAGGAATTTAGAATTGGGTGTTCAAA 58.559 34.615 0.00 0.00 0.00 2.69
1310 1395 6.014669 CCAGGAATTTAGAATTGGGTGTTCAA 60.015 38.462 0.00 0.00 0.00 2.69
1311 1396 5.480073 CCAGGAATTTAGAATTGGGTGTTCA 59.520 40.000 0.00 0.00 0.00 3.18
1312 1397 5.714806 TCCAGGAATTTAGAATTGGGTGTTC 59.285 40.000 0.00 0.00 0.00 3.18
1313 1398 5.650283 TCCAGGAATTTAGAATTGGGTGTT 58.350 37.500 0.00 0.00 0.00 3.32
1314 1399 5.269554 TCCAGGAATTTAGAATTGGGTGT 57.730 39.130 0.00 0.00 0.00 4.16
1315 1400 5.302823 GGATCCAGGAATTTAGAATTGGGTG 59.697 44.000 6.95 0.00 0.00 4.61
1316 1401 5.458595 GGATCCAGGAATTTAGAATTGGGT 58.541 41.667 6.95 0.00 0.00 4.51
1317 1402 4.520492 CGGATCCAGGAATTTAGAATTGGG 59.480 45.833 13.41 0.00 0.00 4.12
1318 1403 4.022849 GCGGATCCAGGAATTTAGAATTGG 60.023 45.833 13.41 0.00 0.00 3.16
1319 1404 4.022849 GGCGGATCCAGGAATTTAGAATTG 60.023 45.833 13.41 0.00 34.01 2.32
1320 1405 4.145052 GGCGGATCCAGGAATTTAGAATT 58.855 43.478 13.41 0.00 34.01 2.17
1321 1406 3.138283 TGGCGGATCCAGGAATTTAGAAT 59.862 43.478 13.41 0.00 40.72 2.40
1322 1407 2.507886 TGGCGGATCCAGGAATTTAGAA 59.492 45.455 13.41 0.00 40.72 2.10
1323 1408 2.123589 TGGCGGATCCAGGAATTTAGA 58.876 47.619 13.41 0.00 40.72 2.10
1324 1409 2.638480 TGGCGGATCCAGGAATTTAG 57.362 50.000 13.41 0.00 40.72 1.85
1340 1425 1.271054 CCATATGGTAGGAGCAGTGGC 60.271 57.143 14.09 0.00 41.61 5.01
1341 1426 2.301296 CTCCATATGGTAGGAGCAGTGG 59.699 54.545 21.28 6.55 44.37 4.00
1342 1427 3.674528 CTCCATATGGTAGGAGCAGTG 57.325 52.381 21.28 0.00 44.37 3.66
1408 1493 0.467290 ATGTTGTTGGAGCCACGGTT 60.467 50.000 0.00 0.00 0.00 4.44
1498 1583 8.394971 TGAGCTTCTTCAATGTCATTAGAAAA 57.605 30.769 10.57 7.81 0.00 2.29
1592 1677 1.442526 GCGAGGGTCAATGGCATCAG 61.443 60.000 0.00 0.00 0.00 2.90
1717 1804 4.487714 TCCAACAATAGACATGGTCCTC 57.512 45.455 0.00 0.00 34.50 3.71
1750 1841 3.257933 GCCAGAGTTGTCTTGCCG 58.742 61.111 0.00 0.00 35.78 5.69
1806 1897 5.291128 CGAGATACGGAAACAAAAGCTACAT 59.709 40.000 0.00 0.00 38.46 2.29
1825 1916 1.071385 GCCATGTCAGGATTCCGAGAT 59.929 52.381 0.00 0.00 0.00 2.75
1855 1946 9.793259 TTGTCAAGTTCATATAAGACCTTCTTT 57.207 29.630 0.00 0.00 37.89 2.52
2035 2291 5.952526 AATAAAACTTAGTTGGGACACGG 57.047 39.130 0.00 0.00 39.29 4.94
2098 3103 9.806203 CATAATTTGAAGAGGCATATGAAACAA 57.194 29.630 6.97 1.12 0.00 2.83
2104 3109 6.978338 AGTGCATAATTTGAAGAGGCATATG 58.022 36.000 0.00 0.00 31.92 1.78
2328 3371 1.768870 ACTACCAAGGCAGTTGTCAGT 59.231 47.619 0.00 0.00 33.87 3.41
2381 3424 8.918116 TCACTAGAAGAGCAACATACATTAGAT 58.082 33.333 0.00 0.00 0.00 1.98
2387 3430 6.530019 TCATCACTAGAAGAGCAACATACA 57.470 37.500 0.00 0.00 0.00 2.29
2436 3479 7.111247 AGAGTTTTCTAGAGTCATCATCAGG 57.889 40.000 0.00 0.00 0.00 3.86
2489 3532 3.332919 CTCCAACTCATCAGGACACTTG 58.667 50.000 0.00 0.00 0.00 3.16
2545 3588 4.033709 AGTGATGATGGCTAGTGGTACTT 58.966 43.478 0.00 0.00 0.00 2.24
2573 3616 5.163343 TGGACCATCGCTAGCTAAAATACTT 60.163 40.000 13.93 0.00 0.00 2.24
2588 3631 4.948847 TGATCTGTTTATCTGGACCATCG 58.051 43.478 0.00 0.00 0.00 3.84
2589 3632 5.238214 GCTTGATCTGTTTATCTGGACCATC 59.762 44.000 0.00 0.00 0.00 3.51
2596 3639 6.506500 ACTTTGGCTTGATCTGTTTATCTG 57.493 37.500 0.00 0.00 0.00 2.90
2601 3644 6.006449 AGTGATACTTTGGCTTGATCTGTTT 58.994 36.000 0.00 0.00 0.00 2.83
2609 3652 2.749621 GTCCCAGTGATACTTTGGCTTG 59.250 50.000 0.00 0.00 0.00 4.01
2671 3714 3.054875 TCTCTGCATGTCCTTTGCACTAT 60.055 43.478 0.00 0.00 44.73 2.12
2778 3822 6.075315 TCCATATCAATCGGTCTCTCCTTAA 58.925 40.000 0.00 0.00 0.00 1.85
2949 3993 5.069914 ACAAATCAAGCACCATATCATGCAT 59.930 36.000 9.76 0.00 44.59 3.96
2970 4014 3.322541 TCACTCGACAGGGAACATAACAA 59.677 43.478 0.00 0.00 0.00 2.83
2987 4031 9.463443 AATATTGTAGCAAAGTTTTGTTCACTC 57.537 29.630 6.48 0.00 40.24 3.51
3027 4071 4.630069 GCTGTGCGAAATAGGTTTTCTCTA 59.370 41.667 0.00 0.00 0.00 2.43
3029 4073 3.188460 TGCTGTGCGAAATAGGTTTTCTC 59.812 43.478 0.00 0.00 0.00 2.87
3032 4076 3.305335 CCTTGCTGTGCGAAATAGGTTTT 60.305 43.478 0.00 0.00 0.00 2.43
3044 4088 0.108138 ATCTACGACCCTTGCTGTGC 60.108 55.000 0.00 0.00 0.00 4.57
3065 4109 6.525976 GCTCTGACATGCTATTTTGAAAAGAC 59.474 38.462 0.00 0.00 0.00 3.01
3122 4166 3.185246 ACAACAGACCTCACTTGTGAG 57.815 47.619 20.36 20.36 35.78 3.51
3193 4237 6.661805 ACCTTCCAAATCCAATACACGTAAAT 59.338 34.615 0.00 0.00 0.00 1.40
3280 4324 3.049344 CCTCTTAGCCCCAGATACCTTT 58.951 50.000 0.00 0.00 0.00 3.11
3315 4359 1.062734 TCCTATTTCCACGGGGAGCTA 60.063 52.381 6.46 1.43 46.01 3.32
3384 4428 4.067896 ACACTTGTTGGAATCACTGCTAG 58.932 43.478 0.00 0.00 0.00 3.42
3418 4480 3.925299 TGCATTTTGGCATATCAAACGTG 59.075 39.130 0.00 0.00 39.25 4.49
3433 4495 0.179156 CGCTGAATCGGCTGCATTTT 60.179 50.000 12.66 0.00 32.89 1.82
3451 4513 0.461339 CCCGATCCCAACTGGTAACG 60.461 60.000 0.00 0.00 42.51 3.18
3473 4538 2.857152 CAGCTCTTCTAATGACGTCAGC 59.143 50.000 24.41 17.91 0.00 4.26
3501 4566 3.327757 AGCTCTTTCACATCCACCAGTAA 59.672 43.478 0.00 0.00 0.00 2.24
3504 4569 2.486472 AGCTCTTTCACATCCACCAG 57.514 50.000 0.00 0.00 0.00 4.00
3586 4681 4.344104 CAGGGACACCACCAAAGAATTAT 58.656 43.478 0.00 0.00 40.13 1.28
3674 4772 1.001503 GGGCATCCAACCATCCCAA 59.998 57.895 0.00 0.00 36.96 4.12
3687 4785 3.590466 GAAGCTGTGGGGTGGGCAT 62.590 63.158 0.00 0.00 0.00 4.40
3760 9511 3.440154 GGAGGAGAGGAGGGGAAATGATA 60.440 52.174 0.00 0.00 0.00 2.15
3797 9548 1.867919 CTTCCGGTCGCACTCTGTCT 61.868 60.000 0.00 0.00 0.00 3.41
3809 9561 3.506067 GGATTTGAATGTCAACTTCCGGT 59.494 43.478 0.00 0.00 35.89 5.28
3858 9610 4.898861 AGATTTGTTTACCCAAAGCCAGAA 59.101 37.500 0.00 0.00 40.63 3.02
3872 9625 3.002656 CACGAGTGTGCTGAGATTTGTTT 59.997 43.478 0.00 0.00 39.67 2.83
3907 9662 1.345415 GGAATGCATTAGGGCCAATGG 59.655 52.381 12.97 0.00 36.58 3.16
3915 9670 4.646040 TCTCAAACATGGGAATGCATTAGG 59.354 41.667 12.97 0.94 0.00 2.69
3960 9715 4.545376 TGGAAATATAGATGGCCCCATGAT 59.455 41.667 4.19 1.03 36.70 2.45
3964 9719 2.039746 CGTGGAAATATAGATGGCCCCA 59.960 50.000 0.00 0.00 0.00 4.96
3977 9732 1.202698 GGCATAGCTCCTCGTGGAAAT 60.203 52.381 7.75 1.78 42.66 2.17
4034 9789 0.104304 GGTCACCGCCGACAATATCT 59.896 55.000 5.03 0.00 37.66 1.98
4123 9880 4.081198 CCTCCTTGCACTTATCTGAAGAGT 60.081 45.833 0.00 0.00 0.00 3.24
4150 9907 1.455412 TGCCTCAGCACAACATCCA 59.545 52.632 0.00 0.00 46.52 3.41
4200 9957 1.353076 GACCCACGAATGGTACGAAC 58.647 55.000 0.00 0.00 45.66 3.95
4216 9982 4.041075 AGAAGAAACCTGAGAGAAAGGACC 59.959 45.833 0.00 0.00 38.27 4.46
4315 10081 2.031245 CGCATAATTAAATCCAGCGGCA 60.031 45.455 1.45 0.00 40.00 5.69
4320 10086 2.584791 GCCGCGCATAATTAAATCCAG 58.415 47.619 8.75 0.00 0.00 3.86
4350 10116 1.227853 AGGGTGAACACGTGGCTTC 60.228 57.895 21.57 15.56 0.00 3.86
4404 10171 0.745128 TGCTTCCACGAAACGGTTGT 60.745 50.000 0.00 0.00 0.00 3.32
4455 10235 0.829602 GGATCTCATCCTCGCCCTGA 60.830 60.000 0.00 0.00 46.19 3.86
4589 10369 1.916777 CTGGAAGGTGTACGGGGGT 60.917 63.158 0.00 0.00 0.00 4.95
4788 10568 2.922503 TGTGAGGAGCTTGCCCGA 60.923 61.111 0.00 0.00 0.00 5.14
4813 10593 3.207265 TGTGAGGAGCTTGCAACTTAA 57.793 42.857 0.00 0.00 0.00 1.85
4884 10669 5.443230 TTAGGACAGTGATCAGAGAGAGA 57.557 43.478 0.00 0.00 0.00 3.10
4885 10670 6.522625 TTTTAGGACAGTGATCAGAGAGAG 57.477 41.667 0.00 0.00 0.00 3.20


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.